Pedicle screw instrumentation of the upper cervical spine is rarely performed in trauma surgery because of the risk of damaging neurovascular structures. We report successful treatment of an unstable hangman's fracture with posterior pedicle screw fixation using Iso-C3D fluoroscopy-based computer navigation guidance. Postoperative computed tomographic images confirmed accurate placement of the pedicle screws. The navigation system is useful, especially in an unstable upper cervical spine injury where the likelihood of change in the inter-segmental relationship is maximal before and after positioning for surgery. The navigation system has the advantage of data acquisition after patient positioning, thus making safe pedicle fixation of the C1 and C2 vertebrae possible despite fractured posterior elements.